Protein Property Analyzer
Paste any real amino-acid sequence. Computes MW, pI, GRAVY, aromaticity, extinction coefficient, net charge, and composition.
Peptide / Antimicrobial Property Calculator
Net charge, GRAVY, hydrophobic moment (Eisenberg 1984 amphipathicity method), and Boman index.
Codon Optimizer
Reverse-translates using real host-preferred codon tables, reports GC% and scans for restriction sites.
Pairwise Sequence Alignment
Real global alignment (Needleman-Wunsch DP) — choose simple scoring (+1/−1/−2) or the real published BLOSUM62 substitution matrix.
DNA / RNA Toolkit
Real reverse complement, transcription, GC%, GC skew, melting temperature (Wallace rule + GC% method), 6-frame translation (full 64-codon table), and ORF detection (ATG…stop, min 30 nt).
Restriction Digest Mapper
Scans against a real 30-enzyme recognition-site database (standard Type II cloning enzymes) and computes actual fragment sizes after a full linear digest.
Motif & Cleavage Site Scanner
Regex scan of a protein sequence against 20 real, literature-standard motifs: PTM sites (N-glycosylation, phosphorylation consensus sites), protease cleavage sites (thrombin, TEV, Factor Xa, caspases, furin, enterokinase, PreScission), and trafficking signals (KDEL, NLS, RGD, myristoylation).
Hydropathy & Complexity Profile
Real sliding-window Kyte-Doolittle hydropathy plot (used to spot transmembrane helices and surface loops) plus a Shannon entropy complexity track (flags repetitive / low-complexity regions).
Primer Designer
Generates forward and reverse primers from a DNA template with real Tm (GC% method), GC content, 3′ GC-clamp check, and simple run/self-complementarity screening.
Live Database Lookup — Free Public APIs
⚠ Unlike every other tab on this page, these three tools call real external services over the internet — UniProt (EMBL-EBI), RCSB PDB, and Meta's public ESM Atlas structure-prediction API. All three are free and require no API key. Your query text is sent to that third party's servers (not to Lakshmi Biosciences). If your network blocks these domains, the call will fail gracefully with an error message.
UniProt Search
Real-time search of the UniProt knowledgebase (EMBL-EBI) — returns actual accessions, protein names, organisms, and sequences.
RCSB PDB Structure Search
Real full-text search against the RCSB Protein Data Bank (confirmed working live) — returns actual deposited structure IDs, titles, method, and resolution.
ESMFold Structure Prediction (Live)
Sends your sequence to Meta AI's public ESM Atlas API for real GPU-backed structure prediction. ⚠ Note: Meta's api.esmatlas.com endpoint has a publicly reported, ongoing SSL/reliability issue (independent of this page) — if the live call below fails, use the direct link to their own working web form instead.
Volcano Plot (RNA-seq Differential Expression)
Paste real differential-expression results (gene, log2FoldChange, p-value — CSV/TSV, one gene per line, header row optional). Computes -log10(p), classifies significance, and renders a real interactive scatter plot.
Expression Heatmap
Paste a real expression matrix (first row = sample names, first column = gene names, CSV). Computes real per-gene z-score normalization and renders a diverging-color heatmap.
Literature Search (PubMed)
⚠ Confirmed by testing: NCBI's eutils API doesn't send CORS headers, so direct browser access is permanently blocked (this is on NCBI's server, not fixable client-side). The reliable path is the direct link below, which opens your exact query on pubmed.ncbi.nlm.nih.gov. A live attempt still runs first in case NCBI changes this.
🤖 AI Assistant — Describe What You Want
Real LLM (Claude) automation, live — describe your task in plain English and it routes to the right tool, fills in the inputs, and runs it automatically. Also works as a research assistant: paste any result from another tab and ask it to explain what it means.
⚠ Important: this feature calls the Anthropic API directly from the page. That call is designed to work only when this page is rendered inside Claude.ai's own artifact preview (which handles authentication automatically) — I can't fully verify that path from my sandbox, so please test it in-chat and tell me the result. It will definitely fail with a CORS error if you download this file and open it standalone in your own browser (confirmed by testing) — unlike the UniProt/RCSB/PubMed tools above, which are public APIs and work anywhere.
Automated Task Router
e.g. "analyze this sequence: MKTAYIAKQRQ..." · "search UniProt for insulin" · "find literature on BRCA1 breast cancer" · "check this DNA for restriction sites: ATGGAATTC..." · "design primers for ATGAAAACC..."
Result Interpreter
Paste any result text (from another tab's "Download result") and ask the LLM to explain it in plain English, flag anything notable, and suggest next steps.
Protein–Peptide Binding Compatibility Screen
⚠ Not a docking simulation — real physical docking (AutoDock Vina, HDOCK, AlphaFold-Multimer) needs actual 3D coordinates and GPU/HPC compute, out of scope for a browser tool. This instead computes real, published sequence-level compatibility signals: electrostatic complementarity, hydrophobicity correlation, size ratio, and interface hot-spot residue enrichment (Trp/Tyr/Arg — the "O-ring" hot-spot residues identified by Bogan & Thorn, 1998). Use it as an early triage heuristic only, then confirm real candidates with actual docking/experiments.